PSB 2006
Michael Ashburner, "Ontologies for biologists - A community model for the annotation of genomic data"
One of the originators of the GO ontology, Dr. Ashburner talked about the intial planning and development of the GO ontology and how it (and everything in bioinformatics) should follow the "Manifesto of liberation of bioinformatics":
-Be open source.
-Use open standards.
-Make data and code available without constraint.
-Involve your community.

He also noted that in the near future there will be links between the three main categories in the GO ontology (geneontology.org) meaning there will be interrelationships between molecular functions, biological processes, and locations. For me, this means more headache for developing methods that must utilize the now more complex (interrelated) heirarchy of the ontology. It seems from this talk that the future is more and more ontologies that are all linked together somehow. He mentions that there are many specialized ontologies that are popping up that augment GO. Think things like neuro ontology and ligand ontology (author's ideas not Dr. Ashburner's); moreover these ontologies are linked and launched through efforts like the national center for biomedical ontology.

Perhaps the most successful type of new ontology (well I'll assume it's the most successful because it's the only other one he got into) is Sequence Ontology or (SO). Here sequences are annotated with different features for different locations on the sequence with a defined ontological heirarchy. He mentions attributes encompassing sequence attributes, mutational consequences, and chromosomal variation.
All in all it was an interesting talk about the future of biological ontologies, which, in my view, is a pretty much thankless job but very important to the field. Think over 1000 citations on Scholar.